Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise
Searched keyword : Metabolomics
Related people (3)
After a PhD in informatics on graph analysis (metabolic networks and sRNA-mRNA interaction graphs) at the LaBRI (Université de Bordeaux), I joined the DSIMB team (INTS) for a post-doc on structural modeling. Then, I performed a second post-doc at Metagenopolis – INRA Jouy-en-Josas, where I was initiated to the analysis of metagenomic data. I was recruited at the HUB in 2015, and since I pursue the development of methods dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, the statistics, the protein structural modeling and the graph analysis.
AlgorithmicsClusteringGenome assemblyGenomicsMetabolomicsModelingNon coding RNASequence analysisStructural bioinformaticsTargeted metagenomicsDatabaseGenome analysisBiostatisticsProgram developmentScientific computingDatabases and ontologiesExploratory data analysisData and text miningIllumina HiSeqComparative metagenomicsRead mappingIllumina MiSeqSequence homology analysisGene predictionMultidimensional data analysisSequencingShotgun metagenomics
- Evaluation of a novel mouse model for Primary Antibody Deficiency (PAD)(Lise HUNAULT - Antibodies in Therapy and Pathology) - In Progress
- Measles virus type 1 infection disturbs the mitochondrial network leading to type I interferon production through the RNA polymerase III/RIG-I pathway(Jean-Pierre VARTANIAN - Department of Virology) - Awaiting Publication
- Comparative analysis of choanoflagellate proteomic data(Thibaut BRUNET - Other) - Closed
Hugo Varet is a biostatistician engineer from the Ensai (Ecole Nationale de la Statistique et de l’Analyse de l’Information) and has been recruited in 2013 by the Transcriptome & Epigenome Platform of the Biomics Pole. Late 2014 he obtained a permanent position at the Bioinformatics & Biostatistics Hub and has been detached to the platform to continue the statistical analyses of RNA-Seq data and develop R pipelines and Shiny applications that help in this task. One of them is named SARTools and is available on GitHub: https://github.com/PF2-pasteur-fr/SARTools. In December 2019 he left the Biomics Platform and joined the Bioinformatics & Biostatistics Hub as a core-member.
MetabolomicsModelingSequence analysisStatistical inferenceTranscriptomicsBiostatisticsScientific computingApplication of mathematics in sciencesExploratory data analysisHigh Throughput ScreeningClinical research
- Evaluation in cellulo of the impact of insecticide usage on arbovirus population(VALLET THOMAS - Viral Populations and Pathogenesis) - In Progress
- Analysis of the molecular pathways induced by the activation of the Nod2 receptor by MDP in hypothalamic neurons(Ilana GABANYI - Perception and Memory) - Pending
- Characterization of a broad spectrum chemical inhibitor targeting the endocytic pathway to prevent bacterial intoxications.(Eléa PAILLARES - Bacterial Toxins) - In Progress
A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, knowledge inference, ontologies and data visualisation.
AlgorithmicsData VisualizationMetabolomicsModelingPathway AnalysisPhylogeneticsSystems BiologyTool DevelopmentDatabaseProgram developmentScientific computingDatabases and ontologiesApplication of mathematics in sciencesSofware development and engineeringData and text miningEvolutionData integrationGraph theory and analysisWorkflow and pipeline developmentDiscrete and numerical optimization
VirusHuman Immunodeficiency virus (HIV)
- Modeling mitochondrial metabolism dormant Cryptococcus neoformans(Benjamin HOMMEL - Molecular Mycology) - Closed
- Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment(Alice MEIGNIÉ - Viral Genomics and Vaccination) - Closed
- Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation(Olivier GASCUEL - Evolutionary Bioinformatics) - Closed
Related projects (4)
The aim of the project is to create a viewer that will help visualisation and correlation between genomic, transcriptomic, proteomic and metabolomic data generated by the comparison of amastigote and promastigote stages of the Leishmania donovani parasite.
Innate lymphoid cells (ILCs) are the most recently identified components of the innate immune system. ILCs colonize different tissue sites and react promptly to microenvironmental perturbations. Due to their high plasticity, ILCs can shape their functional output in response to local cues. As such, ILCs play roles under homeostatic conditions and in the context of infection, chronic inflammation, metabolic diseases and cancer. Diverse ILC subsets (NK cells, ILC2) have been shown to regulate the metabolic homeostasis. Metabolic states affect cellular functions and have been shown to play an important role in the regulation of adaptive immunity. In contrast, almost nothing is known about innate lymphocytes metabolism and the importance of energy regulation for ILC function. This project will study metabolic profiles in human ILC subsets under diverse environmental conditions. Enhancing or interfering with ILC activity could ultimately represent a novel useful therapy for chronic inflammatory diseases.
We have shown that chronic stress impact gut microbiota and leads also to metabolomic abnormalitites . We want here to decipher whether particular gut bacterial species could be directly link to the metabolism differences we observed.
Energy demands vary widely depending on cellular activation states. Here we perform an integrated bioenergetic analysis (epigenetic, transcriptomic and metabolomic) of the human CD56Br and CD56Dim natural killer (NK) cell subsets under steady-state conditions and after cytokine activation. We found that CD56Dim NK cells were metabolically active at steady state, but that both subsets increased bioenergetic properties upon priming with IL-15, with metabolic profiles similar to tonsillar NK cells. In contrast, IL-12/IL-18-induced cell activation promoted a dichotomous response with an elevated respiratory and functional capacity in CD56Br NK cells versus a metabolic switch towards glycolysis and reduced IFN-γ production in CD56Dim NK cells. The latter was associated with mitochondria fragmentation; inhibition of which increased IFN-γ production. Polarized mitochondria were identified with the CD57+ CD56Dim NK cell subset, thereby identifying a potential signature for NK cell functional maturation. We propose mitochondrial remodeling as a key regulator of NK cell function.